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Sample GSM329402 Query DataSets for GSM329402
Status Public on Oct 16, 2008
Title Embryos injected with 50uM coMO biological repl. 2
Sample type RNA
 
Source name 72hpf zebrafish embryos
Organism Danio rerio
Characteristics wild type
control morpholinos
Treatment protocol When embryo reached 72hpf they were euthanized in MS222 and put in RNAlater solution at 4°C overnight. The samples were stored until RNA isolation at -20°C
Growth protocol Eggs were pooled from different aquaria, washed with a E3 medium and injected with ERbeta2 MO or coMO at 50uM until the 4 cell stage. After they were raised in petri dishes until 72hpf at 28°C.
Extracted molecule total RNA
Extraction protocol RNA isolation was performed with Rneasy Mini Kit, Qiagen, according to the manufacturer's instructions.
Label biotin
Label protocol biotin-labeling using a IVT Labeling Kit (Affymetrix Inc.)
 
Hybridization protocol Affymetrix Gene Expression protocol using Fragmentation Buffer (Affymetrix Inc., P/N 900371), Hybridization Mix (Affymetrix Inc., P/N 900720), Hybridization Controls and Control Oligonucleotide B2 (Affymetrix Inc., P/N 900454). Arrays were washed using an Affymetrix Fluidics Station 450 (FS450_0004 protocol)
Scan protocol Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.), according to manufacturer
Description gene expression in 72hpf zebrafish embryos
Data processing Raw data processing was performed using the Affymetrix AGCC software. After hybridization and scanning, probe cell intensities were calculated by means of the MAS5 algorithm. The data were then analyzed with Genespring. The data were normalized per chip (50th percentil) and per gene (to median). They were finally filtered by fold change (fold change data files are on the Series record).
 
Submission date Oct 10, 2008
Last update date Oct 15, 2008
Contact name Mirjam Föhlicher
E-mail(s) mirjam.froehlicher@eawag.ch
Organization name eawag
Street address überlandstrasse 133
City Dübendorf
ZIP/Postal code 8600
Country Switzerland
 
Platform ID GPL1319
Series (2)
GSE13158 The role of ERbeta2 in zebrafish neuromasts development 50uM
GSE13771 The role of ERbeta2 in zebrafish neuromasts development

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 564.517 P 0.000581214
AFFX-BioB-M_at 750.163 P 5.16732e-05
AFFX-BioB-3_at 453.373 P 0.000126798
AFFX-BioC-5_at 1283.36 P 6.02111e-05
AFFX-BioC-3_at 1325.51 P 4.42873e-05
AFFX-BioDn-5_at 3210.62 P 4.42873e-05
AFFX-BioDn-3_at 6539.01 P 5.16732e-05
AFFX-CreX-5_at 18804.5 P 4.42873e-05
AFFX-CreX-3_at 33741.4 P 4.42873e-05
AFFX-DapX-5_at 263.018 P 0.000146581
AFFX-DapX-M_at 766.398 P 0.000195116
AFFX-DapX-3_at 1367.48 P 5.16732e-05
AFFX-LysX-5_at 45.0281 P 0.0182806
AFFX-LysX-M_at 168.282 P 0.036569
AFFX-LysX-3_at 297.387 P 9.4506e-05
AFFX-PheX-5_at 36.5984 A 0.116113
AFFX-PheX-M_at 59.1963 M 0.0429619
AFFX-PheX-3_at 255.274 P 0.000509415
AFFX-ThrX-5_at 112.905 P 0.0166701
AFFX-ThrX-M_at 197.087 P 0.000972149

Total number of rows: 15617

Table truncated, full table size 572 Kbytes.




Supplementary file Size Download File type/resource
GSM329402.CEL.gz 2.0 Mb (ftp)(http) CEL
GSM329402.CHP.gz 85.9 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file
Processed data are available on Series record

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